Drug response consistency in CCLE and CGP.
Ontology highlight
ABSTRACT:
SUBMITTER: Bouhaddou M
PROVIDER: S-EPMC5554885 | biostudies-literature | 2016 Nov
REPOSITORIES: biostudies-literature
Publications
Drug response consistency in CCLE and CGP.
Bouhaddou Mehdi M DiStefano Matthew S MS Riesel Eric A EA Carrasco Emilce E Holzapfel Hadassa Y HY Jones DeAnalisa C DC Smith Gregory R GR Stern Alan D AD Somani Sulaiman S SS Thompson T Victoria TV Birtwistle Marc R MR
Nature 20161101 7631
Similar Datasets
Project description:Accurate quantification of drug effects is crucial for identifying pharmaceutically actionable cancer vulnerabilities. Current cell viability-based measurements often lead to biased response estimates due to varying growth rates and experimental artifacts that explain part of the inconsistency in high-throughput screening results. We developed an improved drug scoring model, normalized drug response (NDR), which makes use of both positive and negative control conditions to account for differences in cell growth rates, and experimental noise to better characterize drug-induced effects. We demonstrate an improved consistency and accuracy of NDR compared to existing metrics in assessing drug responses of cancer cells in various culture models and experimental setups. Notably, NDR reliably captures both toxicity and viability responses, and differentiates a wider spectrum of drug behavior, including lethal, growth-inhibitory and growth-stimulatory modes, based on a single viability readout. The method will therefore substantially reduce the time and resources required in cell-based drug sensitivity screening.
| S-EPMC6978361 | biostudies-literature
Project description:AimsThe aim of this study was to explore the level of agreement on drug-drug interaction (DDI) information listed in three major online drug information resources (DIRs) in terms of: (1) interacting drug pairs; (2) severity rating; (3) evidence rating; and (4) clinical management recommendations.MethodsWe extracted information from the British National Formulary (BNF), Thesaurus and Micromedex. Following drug name normalisation, we estimated the overlap of the DIRs in terms of DDI. We annotated clinical management recommendations either manually, where possible, or through application of a machine learning algorithm.ResultsThe DIRs contained 51 481 (BNF), 38 037 (Thesaurus) and 65 446 (Micromedex) drug pairs involved in DDIs. The number of common DDIs across the three DIRs was 6970 (13.54% of BNF, 18.32% of Thesaurus and 10.65% of Micromedex). Micromedex and Thesaurus overall showed higher levels of similarity in their severity ratings, while the BNF agreed more with Micromedex on the critical severity ratings and with Thesaurus on the least significant ones. Evidence rating agreement between BNF and Micromedex was generally poor. Variation in clinical management recommendations was also identified, with some categories (i.e., Monitor and Adjust dose) showing higher levels of agreement compared to others (i.e., Use with caution, Wash-out, Modify administration).ConclusionsThere is considerable variation in the DDIs included in the examined DIRs, together with variability in categorisation of severity and clinical advice given. DDIs labelled as critical were more likely to appear in multiple DIRs. Such variability in information could have deleterious consequences for patient safety, and there is a need for harmonisation and standardisation.
| S-EPMC9545693 | biostudies-literature
Project description:Reactivation of the multi-subunit ribonucleoprotein telomerase is the primary telomere maintenance mechanism in cancer, but it is rate-limited by the enzymatic component, telomerase reverse transcriptase (TERT). While regulatory in nature, TERT alternative splice variant/isoform regulation and functions are not fully elucidated and are further complicated by their highly diverse expression and nature. Our primary objective was to characterize TERT isoform expression across 7887 neoplastic and 2099 normal tissue samples using The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression Project (GTEx), respectively. We confirmed the global overexpression and splicing shift towards full-length TERT in neoplastic tissue. Stratifying by tissue type we found uncharacteristic TERT expression in normal brain tissue subtypes. Stratifying by tumor-specific subtypes, we detailed TERT expression differences potentially regulated by subtype-specific molecular characteristics. Focusing on β-deletion splicing regulation, we found the NOVA1 trans-acting factor to mediate alternative splicing in a cancer-dependent manner. Of relevance to future tissue-specific studies, we clustered cancer cell lines with tumors from related origin based on TERT isoform expression patterns. Taken together, our work has reinforced the need for tissue and tumour-specific TERT investigations, provided avenues to do so, and brought to light the current technical limitations of bioinformatic analyses of TERT isoform expression.
| S-EPMC8070023 | biostudies-literature
Project description:Drug-drug interactions (DDIs) can either enhance or diminish the positive or negative effects of the associated drugs. Multiple drug combinations create difficulties in identifying clinically relevant drug interactions; this is why electronic drug interaction checkers frequently report DDI results inconsistently. Our paper aims to analyze drug interactions in cardiovascular diseases by selecting drugs from pharmacotherapeutic subcategories of interest according to Level 2 of the Anatomical Therapeutic Chemical (ATC) classification system. We checked DDIs between 9316 pairs of cardiovascular drugs and 25,893 pairs of cardiovascular and other drugs. We then evaluated the overall agreement on DDI severity results between two electronic drug interaction checkers. Thus, we obtained a fair agreement for the DDIs between drugs in the cardiovascular category, as well as for the DDIs between drugs in the cardiovascular and other (i.e., non-cardiovascular) categories, as reflected by the Fleiss' kappa coefficients of κ=0.3363 and κ=0.3572, respectively. The categorical analysis of agreement between ATC-defined subcategories reveals Fleiss' kappa coefficients that indicate levels of agreement varying from poor agreement (κ<0) to perfect agreement (κ=1). The main drawback of the overall agreement assessment is that it includes DDIs between drugs in the same subcategory, a situation of therapeutic duplication seldom encountered in clinical practice. Our main conclusion is that the categorical analysis of the agreement on DDI is more insightful than the overall approach, as it allows a more thorough investigation of the disparities between DDI databases and better exposes the factors that influence the different responses of electronic drug interaction checkers. Using categorical analysis avoids potential inaccuracies caused by particularizing the results of an overall statistical analysis in a heterogeneous dataset.
| S-EPMC10975099 | biostudies-literature
Project description:Arabinoxylan-Oligosaccharide Intake changes the microbiota and softens stool consistency without changes in gut transit and metabolic health in healthy adults
| PRJEB32919 | ENA
Project description:Here we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers, namely 16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics, and metabolomics. Using this controlled setting, we find that all omics methods with species resolution in their readouts are highly consistent in estimating relative species abundances across conditions. Furthermore, different omics methods can be complementary in their ability to capture functional changes in response to the drug perturbations. For example, while nearly all omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control and metabolomics revealed a decrease in polysaccharide uptake, likely caused by Bacteroidota depletion. Taken together, our study provides insights into how multi-omics datasets can be utilised to reveal complex molecular responses to external perturbations in microbial communities.
2022-12-13 | PXD036445 | Pride
Project description:Functional MRI is valuable in presurgical planning due to its non-invasive nature, repeatability, and broad availability. Using ultra-high field MRI increases the specificity and sensitivity, increasing the localization reliability and reducing scan time. Ideally, fMRI analysis for this application should identify unreliable runs and work even if the patient deviates from the prescribed task timing or if there are changes to the hemodynamic response due to pathology. In this study, a model-free analysis method-UNBIASED-based on the consistency of fMRI responses over runs was applied, to ultra-high field fMRI localizations of the hand area. Ten patients with brain tumors and epilepsy underwent 7 Tesla fMRI with multiple runs of a hand motor task in a block design. FMRI data were analyzed with the proposed approach (UNBIASED) and the conventional General Linear Model (GLM) approach. UNBIASED correctly identified and excluded fMRI runs that contained little or no activation. Generally, less motion artifact contamination was present in UNBIASED than in GLM results. Some cortical regions were identified as activated in UNBIASED but not GLM results. These were confirmed to show reproducible delayed or transient activation, which was time-locked to the task. UNBIASED is a robust approach to generating activation maps without the need for assumptions about response timing or shape. In presurgical planning, UNBIASED can complement model-based methods to aid surgeons in making prudent choices about optimal surgical access and resection margins for each patient, even if the hemodynamic response is modified by pathology. Hum Brain Mapp 38:3163-3174, 2017. © 2017 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.
| S-EPMC5434844 | biostudies-literature
Project description:The disease Lupus erythematosus (LE), exhibits a variety of clinical manifestations with potentially wide-ranging multi-organ damage to joints, tendons, kidney, lung, heart, blood vessels, central nervous system and skin [1,2] Systemic changes are likely to trigger organ specific manifestation of the disease. Here, we provide the data examined to address the gap in knowledge regarding causes and mechanisms contributing to the autoimmune attack on skin in chronic cutaneous lupus erythematosus (CCLE). The raw gene expression data files (CEL files) are provided with this article [3].
| S-EPMC4459765 | biostudies-literature
Project description:Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.
| S-EPMC10495815 | biostudies-literature
Project description:Cancer cell lines can provide robust and facile biological models for the generation and testing of hypothesis in the early stages of drug development and caner biology. Although clinical trials remain the ultimate scientific testing ground for anticancer therapies, the use of appropriate model systems to explore the molecular basis of drug activity and to identify predictive biomarkers during their development can have a profound effect on the design, cost and ultimate success of new cancer drug development. In order to capture the high degree of genomic diversity in cancer and to identify rare molecular subtypes, we have assembled a collection of >1000 cancer cell lines. These lines have been characterised using whole exome sequencing, genome wide analysis of copy number, mRNA gene expression profiling and DNA methylation analysis (http://cancer.sanger.ac.uk/cell_lines). To further characterise this panel of cell lines we have now compiled data for RNA sequencing. The current study represent data for ~450 of the cell lines in the panel, data for the remaining lines can be accessed via the CGHUB data browser hosted at UCSC. <br>This ArrayExpress record contains only meta-data. Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity. The relevant accessions of the EGA data set is EGAD00001001357 under EGA study accession EGAS00001000828.
2017-09-25 | E-MTAB-3983 | biostudies-arrayexpress